Comparative transcriptomics and metabolomics provide insight into degeneration-related physiological mechanisms of Morchella importuna after long-term preservation

Abstract

Ascomycetes fungi are often prone to degeneration. Agricultural production of the prized ascomycete mushroom Morchella importuna (black morel) typically suffers from reduced yield and malformed ascocarps owing to culture degeneration. This study compared M. importuna cultures subjected to five different long-term preservation treatments, using transcriptomics and metabolomics. Avoiding repeated subculturing in combination with nutrient-limited conditions was found to be the most beneficial method for maintaining the fruiting capability of morels. The expression of the gene sets involved in cysteine and methionine metabolism and nucleocytoplasmic transport was upregulated under nutrient-limited and nutrient-rich conditions, respectively. This increased expression was accompanied by differential accumulation of metabolites involved in nucleobase metabolism. Repeated subculturing triggered dissimilar changes in the functional modules under nutrient-rich and nutrient-limited conditions. A diverse set of cellular biochemical processes related to carbon metabolism were altered by repeated subculturing under nutrient-rich conditions, whereas glycerophospholipid and purine metabolism were key functions affected by repeated subculturing under nutrient-limited conditions. Altogether, metabolic alterations related to sulfur-containing amino-acid biosynthesis, DNA repair, and cellular structural maintenance contributed to improved preservation outcomes in terms of morel fruiting capability. Our findings contribute to a more detailed understanding of the molecular mechanisms related to subculturing and fruiting of ascomycete macrofungi after long-term preservation.

FIGURE 1

Schematic diagram of the experimental design with five long‐term preservation treatments.

FIGURE 2

(A) Venn diagram of transcripts present in the CK and T1–T4 treatments. (B) Principal component analysis (PCA) scatter plot of transcriptional profiles of morel cultures in five preservation treatments. (C) Heat map of gene expression intensity.

FIGURE 3

Differentially expressed genes (DEGs). Comparisons were conducted between cultures grown in the same medium but treated using different preservation methods: T3 versus T2, CK versus T4, and T1 versus T4. Comparisons between cultures treated using the same preservation methods but grown in different media: T2 versus T4, and T3 versus CK.

FIGURE 4

Enrichment of differentially expressed genes (DEGs) in Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways.

FIGURE 5

(A) Principal component analysis (PCA) scatter plot of metabolites in the five preservation treatments. (B) Functional classification of metabolites based on Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway annotation.

FIGURE 6

Differentially accumulated metabolites. Comparisons were conducted between cultures grown in the same medium but treated using different preservation methods: T3 versus T2, CK versus T4, and T1 versus T4. Comparisons between cultures treated using the same preservation methods but grown in different media: T2 versus T4, and T3 versus CK.

FIGURE 7

Enrichment of differentially accumulated metabolites in Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways.